Villa suffered their first defeat of the new Barclays U18 Premier League in bizarre circumstances at Bodymoor Heath.
Harry McKirdy's two goals weren't enough to earn Tony McAndrew's team a share of the spoils.
However, the big turning point of the match came just before half-time when the home side had an effort ruled out following an unusual penalty incident.
After Villa were awarded a spot kick, Khalid Abdo struck the effort against the crossboar.
The Swedish midfielder rammed home the rebound and the referee incorrectly awarded a goal.
Having realised that no other player had touched the ball before Abdo, the official corrected his decision and the effort was disallowed.
Villa were already 2-1 up at this point after McKirdy bagged a brace to wipe out Callum Dyson's opener.
Everton emerged for the second half rejuvenated and levelled the score when Gethin Jones finished from close range on 55 minutes.
Then 15 minutes from time Harry Charsley forced the ball over the line to seal a victory for the Toffees.
VILLA: Grant, R Strain, Wildin, Zazrivec, Lyons-Foster, Toner, O'Brien, McKirdy, T Strain, Abdo, Green. Subs: H Lewis [for McKirdy. 70], Bannister, Taylor [for Toner, 46], O'Hare.